The bootstrap code has a clear division between the core import functionality and the path-based import machinery. The attached patch makes that division explicit by moving the latter into its own module. The module is also frozen, necessarily. In addition to clearly distinguishing the two parts, this division will help with some later work that I'd like to do later with an encapsulated import system abstraction.
The patch uses the name "pathy" throughout, which I'll change to something more descriptive later. I'll also add the news entry then.

Here's an updated patch, with the PEP 489 changes merged in. Only one test isn't passing and it is due to something in the pip that is bundled into ensurepip. I'll work on fixing that when I have some time. I'm sure there's documentation near the bundle that explains how to update it.

Nice, this ties directly into one of the thornier problems in the PEP 432 bootstrapping work, which needs to set up the core import system in Py_BeginInitialization, but delay setting up the rest of it until Py_EndInitialization.
Your patch achieves this by moving everything that belongs in the latter part of the operation to the "import _frozen_path_importer" step.
As far as naming goes, I'd suggest referring to the two import subsystems as "internal imports" and "external imports". The key aspect of builtin and frozen modules is that they're an inherent part of the interpreter itself - if you have an interpreter, you have all of its buitin and frozen modules natively available. By contrast, setting up the external import machinery requires that the interpreter first be configured to appropriately communicate with the host system.

Here's an updated patch with "_pathy.py" changed to "_bootstrap_external.py" (and similar changes with freezing). The patch does not include fixing the venv test (i.e. the bundled pip).
Also, I'll be adding a note to NEWS.

As a compatibility hack for setuptools versions with the issue, I'd suggest
making importlib._bootstrap.setup alias SourceFileLoader back into
importlib._bootstrap, with an explanation and link to back to this issue in
a comment.

This checkin broke the buildbots. If you build trunk then run
./python -bb -m test test_site
the test fails. "-bb" is used by the normal test runner ("make test").
The problem is in the lines
self.assertTrue(os.path.isabs(os__file__),
"expected absolute path, got {}".format(os__file__))
self.assertTrue(os.path.isabs(os__cached__),
"expected absolute path, got {}".format(os__cached__))
os__file__ and os__cached__ are bytes but you're passing them into .format() on a str.

Thanks for pointing this out, Ned. Early on I ran into a problem when running _freeze_importlib without the flag set. However, I expect that it was not necessary after a certain point (e.g. once I had a valid _importlib_external.h). I'll remove the flag as suggested.